Genome Evolution of Mycobacterium leprae
Overview Mycobacterium leprae, the microbial pathogen that causes leprosy, has a genome marked by substantial reductive evolution. M. leprae is a rod-shaped, acid fast, intracellular, and aerobic obligate pathogen that spreads person-to-person via nasal droplets. The obligate pathogen nature of the microbe has made it impossible to grow in vitro, and so it is normally grown in animals, typically mice, for analysis. Leprosy, also known as Hanson's disease, is a disease characterized as chronic infection by M. leprae or M. lepromatosis. The infection causes granuloma formation, similar to those of M. tuberculosis infection, in the respiratory tract mucosa and peripheral nerves. As the infection progresses it causes further damage to the nerves, eyes, limbs, cartilage, and skin; the primary physical sign of infection is skin lesions. In the 1960s there were tens of millions of reported cases, but currently this number is down to about 180,000 cases. Approximately 95% of people are naturally immune to the infection which has severely decreased the danger to public health associated with infection. In fact, many infected patients can be no longer infectious after only two to three weeks of treatment. This progress has been the result of research and international control programs that serve to help us better understand and prevent the disease. One growing priority of these groups was to provide a whole genome sequence of the microbe to give insight into the specifics of this unique organism that will hopefully catalyze the eradication of leprosy. Genome Sequencing The strain of interest was the M. leprae TN strain which was obtained from a nine-banded armadillo. The DNA sequence was assembled using automated analysis of selected cosmids, and a whole genome shotgun approach. After assembling the sequence, the genome was regenerated and bioinformatics was used to identify repetitive elements and other genomic features such as control signals and functional genes. Comparative genomic analysis to homologous species, specifically M. tuberculosis H37Rv, proved an effective approach of associating genes with specific biochemical function of M. leprae. Results The complete genome sequence was 3.27Mb, and had a G/C content of 57.8%. The bioinformatic analysis predicted that there are 1,605 genes encoding protein and 50 genes encoding stable RNA species. Specifically 49.5% of the genome was protein-coding genes that clustered and were often flanked by non-coding regions, approximately 27% contained recognizable pseudogenes assorted randomly, and inactive reading frames that resemble functional genes in Mycobacterium species. Comparatively: M. tuberculosois has a 4.4Mb and over 4,000 genes encoding for proteins. Genomic Decay The process of reductive evolution occurs when an organism undergoes selective pressure and genes become inactivated after the functions aren't needed in highly specific environments. Similar reduction of genome size has been recorded in other human pathogens, most notably Chlamydia. In this case gene deletion is apparently the dominant mode of genome downsizing indicated by the mass presence of non-coding genes and pseudogenes. The inability of M. leprae to acquire DNA because of its highly specialize niche means that it is inable to repair genetic lesions through acquisition of new genes or genetic recombination. The genes encoding for specific M. tuberculosis enzymes such as Nitrate reductase encoded by narGHIJ and an ABC-transporter encoded by modABC have pseudogenes in M. leprae indicating that when the need for a nitrate-pathway, used in anaerobic respiration, was lost the genes stopped being active and acquired subsequent mutations that led to their decay. Genome Reduction The decay of genes does not account for the 1.1Mb decrease in the size of the genomes, which also translated to the loss of approximately 1,000 protein-coding sequences. This comparison is viewed as valid because at one point in the evolution of mycobacterium all species had genomes of approximately 4.4Mb. A proteomic analysis of M.leprae detected 391 soluble protein species, compared to the near 1,800 in M. tuberculosis. The loss of these proteins was consistent with the large number of pseudogenes in M. leprae. Recombination events of repetitive DNA sequences is currently believe to be the primary cause of the genome downsize and the chromosomal rearrangement that characterizes difference in genomes. Not much is known about other M. leprae isolate strains, but it is believed a recent ancestor underwent the majority of genome downsizing and then was disseminated globally after establishing itself as an obligate intracellular pathogen. Different strains of M. leprae will likely contain point mutations and polymorphisms established recently, however the overall genomes should prove nearly homologous if fully sequenced. Conclusion The eradication of leprosy as a public health concern is still a long term goal. The process will involve improved detection and isolation of infected patients, as well as continued implementation of multi-drug therapies to the infected. Although no specific genes for pathogenesis were identified, understanding the function of specific M. leprae proteins and the genes that code them can provide targets for testing of potentially infected individuals and more effective treatments. The findings of the study provides an insight into a microbe that has caused countless deaths, and this knowledge is key to further understanding and prevention. References http://www.ncbi.nlm.nih.gov/pubmed/11826475Eiglmeier K, Parkhill J (2001): The decaying genome of Mycobacterium leprae (PMID: 11826475) Monot M, N Honore (2009): Comparative genomic and phylogeographic analysis of Mycobacterium Leprae (PMID: 19881526) Schuenemann V, Singh P (2013): Genome-Wide comparison of medieval and modern Mycobacterium leprae (PMID: 23765279)